Some 100 trillion microorganisms inhabit and colonize the human gut (Berg, R. D. “The indigenous gastrointestinal microflora.” Trends Microbiol 4:430-5. 14 (1996); Young, V. B., and Schmidt, T. M. “Overview of the gastrointestinal microbiota.” Adv. Exp. Med. Biol. 635:29-40 (2008)). These commensal organisms serve a wide range of functions increasingly recognized as mutualistic and indispensable for the health of the host, including proper digestion, metabolism, and importantly, colonization resistance against pathogens (Guarner, F. “Enteric flora in health and disease.” Digestion 73 Suppl 1:5-12 (2006)). Alterations of gut microbiota have been linked to asthma, immune system development (Cebra, J. J. “Influences of microbiota on intestinal immune system development.” Am. J. Clin. Nutr. 69:1046S-1051S (1999)), and inflammatory bowel disease (Frank, D. N. et al., “Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases.” Proc. Natl. Acad. Sci. U.S.A. 104:13780-13785 (2007)).
Clostridium difficile is a major cause of diarrhea in healthcare settings, accounting for 10-20% of antibiotic-associated diarrhea and most cases of colitis associated with antibiotic use. The mortality for Clostridium difficile infection is estimated at 1-2.5%, contributing to 15,000-30,000 deaths annually in the U.S. (Ananthakrishnan, A. N. “Clostridium difficile infection: epidemiology, risk factors and management,” Nat Rev Gastroenterol Hapatol, 8:17-26 (2011); Parkes, G. C. et al., “The mechanisms and efficacy of probiotics in the prevention of Clostridium difficile-associated diarrhea,” Lancet Infect Dis, 9:237-44 (2009); and O'Keefe, S. J., “Tube feeding, the microbiota, and Clostridium difficile infection,” World J Gastroenterol, 16:139-42 (2010)). Antibiotic-induced perturbation of gut microbiota is widely believed to provide C. difficile an undesirable advantage, allowing it to proliferate and elaborate its toxins in the background of a susceptible flora (see FIG. 16).
C. difficile is under the control of the indigenous gut flora, which suppresses the population size of C. difficile by a factor of nearly 1 billion fold (Wilson, K. H. “The microecology of Clostridium difficile.” Clin. Infect. Dis. 16 Suppl 4:S214-8 (1993); Borriello, S. P., and Barclay, F. E. “An in-vitro model of colonisation resistance to Clostridium difficile infection.” J. Med. Microbiol. 21:299-309 (1986)). Randomly selected bacterial isolates from the gut flora are partially effective in suppressing C. difficile—a few species, including Lactobacilli, Enterococci, some Bifidobacteria and Bacteroides species, have shown varying degrees of inhibitory activity against C. difficile (Borriello, S. P., and Barclay, F. E. 1986. Ibid.; Naaber, P. et al. “Inhibition of Clostridium difficile strains by intestinal Lactobacillus species.” J Med Microbiol 53:551-4 (2004); Rolfe, R. D. et al. “Bacterial interference between Clostridium difficile and normal fecal flora.” J. Infect. Dis. 143:470-475 (1981); Lee, Y. J. et al. “Identification and screening for antimicrobial activity against Clostridium difficile of Bifidobacterium and Lactobacillus species isolated from healthy infant faeces.” Int J Antimicrob Agents 21:340-6 (2003)). However, despite the importance of gut flora in C. difficile pathogenesis, it remains unclear which components of the gut flora are essential for colonization resistance.
For C. difficile to establish infection in the human host, it is generally believed that disruption of gut flora is required. Indeed, antibiotic exposure is the number one risk factor for C. difficile infection. The mechanisms by which antibiotic exposure leads to C. difficile infection are not clear. Almost all antimicrobials have been implicated. Moreover, the basic ecological features of gut flora that is susceptible to C. difficile infection have not been well defined.
Although metronidazole or oral vancomycin is highly effective in suppressing C. difficile, it does not prevent relapse. Indeed, 15 to 30 percent of patients relapse within 3 months following antibiotic therapy (Petrella, L. A. et al. “Decreased Cure and Increased Recurrence Rates for Clostridium difficile Infection Caused by the Epidemic C. difficile BI Strain.” Clin. Infect. Dis (2012); Pepin, J. et al. “Increasing risk of relapse after treatment of Clostridium difficile colitis in Quebec, Canada.” Clin. Infect. Dis. 40:1591-1597 (2005)). Failure to respond to multiple courses of antimicrobial therapy is not uncommon.
Fecal microbiota transplant (FMT) cures >90% of patients suffering from recurrent C. difficile infection (Bakken, J. S. “Fecal bacteriotherapy for recurrent Clostridium difficile infection.” Anaerobe 15:285-9 (2009); Borody, T. J. “‘Flora Power’—fecal bacteria cure chronic C. difficile diarrhea.” Am J Gastroenterol 95:3028-9 (2000); Famularo, G. et al., “Fecal bacteriotherapy or probiotics for the treatment of intestinal diseases?” Am J Gastroenterol 96:2262-4 (2001); Brandt, L. J. et al., “Long-Term Follow-Up of Colonoscopic Fecal Microbiota Transplant for Recurrent Clostridium difficile Infection.” Am. J. Gastroenterol. (2012); Russell, G. et al., “Fecal bacteriotherapy for relapsing Clostridium difficile infection in a child: a proposed treatment protocol.” Pediatrics 126:e239-42.), but FMT has not gained widespread popularity due to the lack of aesthetic appeal and concern of potential infection risks.